User: L. A. Liggett

gravatar for L. A. Liggett
L. A. Liggett120
Reputation:
120
Status:
Trusted
Location:
Broad Institute, Harvard Medical School, Boston Children's
Last seen:
1 year, 1 month ago
Joined:
4 years, 10 months ago
Email:
l*******@broadinstitute.org

Posts by L. A. Liggett

<prev • 73 results • page 1 of 8 • next >
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Comment: C: dNdScv Zero coding substitutions found in this dataset.
... So, I was not paying close attention to the console and it turns out the samples contained too many variants. In the notebook file the error only mentioned that no coding substitutions were found, but in the console it also mentions that too many variants are in each sample. Using max_muts_per_gene ...
written 15 months ago by L. A. Liggett120
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Comment: C: dNdScv Zero coding substitutions found in this dataset.
... Thanks for the response Inigo. I will confirm that there are indeed coding mutations within the data, though my dataset in all is about 200 samples that have been exome sequenced and contain a bit over 10 million identified variants, so I assume there should be plenty of coding substitutions. I rea ...
written 15 months ago by L. A. Liggett120
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dNdScv Zero coding substitutions found in this dataset.
... I have been trying to run Inigo Martincorena's dNdScv on some exome seq data of mine and I am getting the error that zero coding substitutions are found in the dataset. It looks to me that having the data formatted differently from the example dataset is what has often caused this problem, but it lo ...
software error written 15 months ago by L. A. Liggett120 • updated 15 months ago by Inigo Martincorena190
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Comment: C: Convert mouse amino acid location to genomic location
... This works great! But how did you find the protein id instead of the gene id? ...
written 20 months ago by L. A. Liggett120
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Comment: C: Convert mouse amino acid location to genomic location
... This doesn't seem to work for me either. I am trying to get the coordinates for the mouse `DNMT3a R878H` mutation in the question like this: https://rest.ensembl.org/vep/human/hgvs/ENSMUSG00000020661:p.Arg878His?content-type=application/json But this will not return anything. ...
written 20 months ago by L. A. Liggett120
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Comment: C: Convert mouse amino acid location to genomic location
... Thanks Pierre, I did have a look at this but it is unclear how to perform such an analysis for mouse. It looks like the Ensembl API might be able to do it as illustrated [here][1], but how to switch from human to mouse is not clear to me. [1]: https://rest.ensembl.org/documentation/info/assembly ...
written 20 months ago by L. A. Liggett120
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Convert mouse amino acid location to genomic location
... I have amino acid positions for a number of mouse mutations, for example `DNMT3a R878H`. Is there a way to convert this to a genome coordinate such as` chr12:12345`? The Ensembl Rest API seems to be capable of such a task, and when I make a call for a human change it works as shown here: https ...
genome gene written 20 months ago by L. A. Liggett120
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Separate Genome into Tiers
... I've seen the genome separated into tiers based on functionality; something like Tier I: coding and Tier III: non-coding, non-repeating, non-conserved. Is there a way to match these classifications up with actual genomic locations? I am working specifically with mouse at the moment but it would be g ...
genome written 2.4 years ago by L. A. Liggett120
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Comment: C: How to get orthologous sequence
... This actually works pretty well. I grabbed a targeted region of sequence from UCSC with something like this: wget -O - http://genome.ucsc.edu/cgi-bin/das/hg38/dna?segment=%s:%s,%s >> locs\n' % (chrom, low, high) Then used this in UCSC BLAT to find the orthologous region within mouse. (Th ...
written 2.4 years ago by L. A. Liggett120
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Comment: C: How to get orthologous sequence
... This is what I don't know how to do. I can see how the mouse gene can be accessed, but then how to target a particular hotspot within that region and identify its coordinates? ...
written 2.4 years ago by L. A. Liggett120

Latest awards to L. A. Liggett

Popular Question 14 months ago, created a question with more than 1,000 views. For Output AO using bcftools
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Popular Question 20 months ago, created a question with more than 1,000 views. For Output AO using bcftools
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Popular Question 20 months ago, created a question with more than 1,000 views. For Find Mutations Frequencies by Cancer Type
Popular Question 20 months ago, created a question with more than 1,000 views. For Get gene names from ensembl ID or gene region
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Popular Question 2.4 years ago, created a question with more than 1,000 views. For Accounting for off-target reads
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Popular Question 2.4 years ago, created a question with more than 1,000 views. For Find Mutations Frequencies by Cancer Type
Supporter 2.4 years ago, voted at least 25 times.
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Reason for Freebayes Calling Multi-base Variants
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Popular Question 2.8 years ago, created a question with more than 1,000 views. For Lollipop Plot of Variant Locations
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Converting Illumina fastq quality scores to phred
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Converting Illumina fastq quality scores to phred
Scholar 4.2 years ago, created an answer that has been accepted. For A: Running bcbio.rnaseq with correct formula
Scholar 4.4 years ago, created an answer that has been accepted. For A: Running bcbio.rnaseq with correct formula

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